ReadSeq large sequence bug

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Tue Apr 20 10:03:15 EST 1993


There is a bug in the current release of readseq (dated 1Feb93)
which causes it to abort when fed sequences larger than a certain
size, at least when compiled with certain compilers.  If you
feed a sequence of around 5000 base pairs or larger to readseq,
and it aborts (maybe with the message "Segmentation fault") then
you have found the bug.

Here is a temporary correction for that bug.
In the file ureadseq.c, change near top:

#define kStartLength  500
	to:

#define kStartLength  500000   /* 20Apr93 temp. bug fix */
	/* set this value higher than max seq size expected */

then recompile it, and readseq will work on large sequences. 
(tobacco chlorop. gene  acc#Z00044 with  155844 bp for example)

But this isn't a definative bug fix.  It looks like the
memory management code for calloc/malloc/realloc is failing
where it shouldn't.   I will have to look at it more.

-- Don

-- 
Don Gilbert                                     gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405




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